Marine pollution is becoming more and more serious, especially in coastal areas. Because of the sequestration and consequent accumulation of pollutants in sediments (mainly organic compounds and heavy metals), marine environment restoration cannot exempt from effective remediation of sediments themselves. It has been well proven that, after entering into the seawater, these pollutants are biotransformed into their metabolites, which may be more toxic than their parent molecules. Based on their bioavailability and toxic nature, these compounds may accumulate into the living cells of marine organisms. Pollutants bioaccumulation and biomagnification along the marine food chain lead to seafood contamination and human health hazards. Nowadays, different technologies are available for sediment remediation, such as physicochemical, biological, and bioelectrochemical processes. This paper gives an overview of the most recent techniques for marine sediment remediation while presenting sediment-based microbial fuel cells (SMFCs). We discuss the issues, the progress, and future perspectives of SMFC application to the removal of hydrocarbons and metals in the marine environment with concurrent energy production. We give an insight into the possible mechanisms leading to sediment remediation, SMFC energy balance, and future exploitation.